A week after an IT contractor gunned down 12 workers at the Washington Navy Yard, Navy officials began moving to close gaps in the security clearance process, recommending that all police reports involving an individual must be included when a background check is done.

The Navy, in a report released Monday, revealed that the shooter, Aaron Alexis, did not disclose a 2004 arrest or some financial problems when he filled out his application for a security clearance when he joined the Navy as a reservist several years later. And officials said the background report given to the Navy at the time, also failed to reveal that he had shot out the tires of another person’s car during a 2004 dispute in Seattle.

Instead, the report from the Office of Personnel Management, said Aaron Alexis “deflated” the tires, and did not mention the use of a gun.

Defense officials have acknowledged that a lot of red flags were missed in Alexis’ background, allowing him to maintain a secret security clearance and have access to a secure Navy facility despite a string of behavioral problems and brushes with the law. Over the past week, they have been struggling to determine what might have been missed, and what changes could be made in order to try and prevent similar violence in the future.

So far, however, the detailed reviews only underscore how subjective the security checks can be and how difficult it is to predict violent behavior based only on minor conduct issues that could easily be overlooked.

A review of Alexis’ nearly four-year Navy career, ordered last week by Navy Secretary Ray Mabus, revealed that the full scope of the 2004 arrest was not included in the security clearance report.

According to a senior Navy official, the police report included information about Alexis shooting out the tires of another man’s car, after a recurring dispute over parking. Alexis was arrested, charged with malicious mischief, fingerprinted and spent the night in jail. But when he appeared in court the charges were dismissed and he believed the incident was erased from his record.

The OPM report, provided to the Navy, left out the gun in its description of the incident, saying that Alexis deflated the man’s tires in retaliation for the man putting an unknown substance in Alexis’ gas tank. It was not clear Monday who was at fault for the omission. Officials said they didn’t know if the summary provided to the Navy was compiled by OPM, or if it was put together by the company that investigated Alexis for his clearance, USIS, and passed on to OPM.

The discrepancy, however, prompted Mabus to recommend to Defense Secretary Chuck Hagel that all police reports - not just arrests - be included in a security check. He also recommended Monday that the Navy enhance its management of sailor evaluations and fitness reports by assigning more senior officers to oversee them.

Hagel has ordered two sweeping reviews of military security and employee screening programs, and Mabus’ recommendation will be considered as part of those studies.

A senior Navy official said military officials only became aware that a gun was used in the tire incident when they went back through all the records last week, after the Navy Yard shooting. The official was not authorized to discuss the matter publicly by name so spoke on condition of anonymity.

The tragedy has revealed a number of problems with the security clearance system, including its focus on whether someone is a treason threat, rather than a potential killer.

When a check of Alexis’ fingerprints disclosed the Seattle police incident, it triggered a follow-up interview for the security clearance. An OPM memo about the interview included multiple questions about debts he failed to pay and problems with collection agencies. In each case, the memo noted that Alexis was having financial troubles, was arranging repayment plans and only he and his mother knew of the debts.

“The subject does not feel that knowledge of any of his financial issues could be used against him for blackmail or coercion,” the memo said.

The fact that Alexis did not disclose the debts on his security form was dismissed in the memo, which noted that he answered “no” to the questions because he was working on payment plans and thought the issues would be resolved. He also answered “no” to questions about his police record, including whether he had been arrested, charged, convicted or issued a summons, citation or ticket to appear in court in a criminal proceeding.

The OPM memo said Alexis told the investigator he answered “no” to those questions “because the charge was dismissed and he was told by Connell (his attorney) that the charge would be removed from his record.”

The Navy also released other details about Alexis’ troubled service record, including two efforts by his commander to impose non-judicial punishments for various infractions.

The Navy said Alexis failed to report to work because he was in jail for a disorderly conduct arrest outside a nightclub in Georgia in September 2008. His commander ordered the loss of a half-month’s pay for two months and a one-rank demotion, but suspended both punishments because it was Alexis’ first offense.

About a year later, he jumped off some stairs at another nightclub and broke his ankle. His commander demoted him, but Alexis appealed. Another commander later concluded there wasn’t enough evidence that Alexis was drunk, so the punishment was dismissed.

He was arrested again a year later, for discharging a firearm in his apartment. Navy officials began preparing a less-than-honorable discharge, but it was never completed because he said the incident was an accident, and no charges were filed. Several months later he received an honorable discharge from the Navy.

While in hindsight, the string of events could have set off alarm bells within the Navy, officials said Monday that it is difficult even now to see them as a glaring indicator of last week’s shooting rampage.